Molecular Morphology: Deep Phylogeny Using RNA Structures and Related Markers

分子形态学：利用 RNA 结构和相关标记进行深层系统发育

• 批准号: 5453019
• 负责人: Professor Dr. Peter Florian Stadler
• 金额: --
• 依托单位: Lehrstuhl für Bioinformatik
• 依托单位国家: 德国
• 项目类别: Priority Programmes
• 财政年份: 2005
• 资助国家: 德国
• 起止时间: 2004-12-31 至 2011-12-31
• 项目状态: 已结题
• 来源: https://gepris.dfg.de/gepris/projekt/5453019?language=en
• 关键词: Molecular; Morphology; Deep; Phylogeny; Using

We propose a continued re-evaluation of the existing ribosomal RNA data, and other non-coding RNA classes, with secondary-structure-aware methods, focusing on data that will be retrieved by the EST surveys performed by other participating research groups in the DMP. In this context, we will continue to develop and refine algorithms for the derivation of reliable secondary structure models of novel rRNA sequences and other suitable ncRNA classes, as well as develop methods for utilizing the evolution of the secondary structures themselves for reconstructing phylogenies. The autonomous derivation of clade-specific “molecular morphological characters”, such as sequence features, e.g. particularly wellconserved patterns or insertions, from multiple sequence alignments, and phylogenetically informative structural features will be explored. The development and application of a model that accounts for the character evolution of ncRNA secondary structure as a practical structural alignment tool and the consideration of “realistic” mutational events will be of interest. Additionally, nucleotide substitution models that distinguish between conserved and “other” regions, as well as incorporate the slower evolution of the structural elements themselves will be developed. It will be explored whether the structure-based and structure-enhanced phylogenetic methods can be extended to amino acid sequences. Novel and improved software for rRNA based phylogeny will be provided to the research community.

我们建议继续重新评估现有的核糖体RNA数据，和其他非编码RNA类，与二级结构感知的方法，重点是数据，将检索的EST调查进行的其他参与研究小组在ESTA。在这种情况下，我们将继续开发和完善算法，用于推导新的rRNA序列和其他合适的ncRNA类的可靠的二级结构模型，以及开发利用二级结构本身的进化来重建同源性的方法。进化枝特异性的“分子形态特征”，如序列特征，例如特别保守的模式或插入，从多个序列比对，和遗传信息的结构特征的自主推导将被探索。开发和应用的模型，占ncRNA二级结构的字符演变作为一个实用的结构比对工具和考虑“现实”的突变事件将是有意义的。此外，将开发区分保守区域和“其他”区域的核苷酸取代模型，以及结合结构元件本身的较慢进化。将探讨基于结构和结构增强的系统发育方法是否可以扩展到氨基酸序列。新的和改进的软件rRNA为基础的基因组学将提供给研究界。